Job ID = 6627395 SRX = SRX8521378 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:18:32 prefetch.2.10.7: 1) Downloading 'SRR11978230'... 2020-07-14T02:18:32 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:19:48 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:19:49 prefetch.2.10.7: 'SRR11978230' is valid 2020-07-14T02:19:49 prefetch.2.10.7: 1) 'SRR11978230' was downloaded successfully 2020-07-14T02:19:49 prefetch.2.10.7: 'SRR11978230' has 0 unresolved dependencies Read 12636508 spots for SRR11978230/SRR11978230.sra Written 12636508 spots for SRR11978230/SRR11978230.sra 2020-07-14T02:20:44 prefetch.2.10.7: 1) Downloading 'SRR11978231'... 2020-07-14T02:20:44 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:24:01 prefetch.2.10.7: HTTPS download failed 2020-07-14T02:24:01 prefetch.2.10.7: 1) failed to download SRR11978231 2020-07-14T02:24:26 prefetch.2.10.7: 1) Downloading 'SRR11978231'... 2020-07-14T02:24:26 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:24:26 prefetch.2.10.7: Continue download of 'SRR11978231' from 327598029 2020-07-14T02:24:31 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:24:32 prefetch.2.10.7: 'SRR11978231' is valid 2020-07-14T02:24:32 prefetch.2.10.7: 1) 'SRR11978231' was downloaded successfully 2020-07-14T02:24:32 prefetch.2.10.7: 'SRR11978231' has 0 unresolved dependencies Read 12303746 spots for SRR11978231/SRR11978231.sra Written 12303746 spots for SRR11978231/SRR11978231.sra 2020-07-14T02:25:28 prefetch.2.10.7: 1) Downloading 'SRR11978232'... 2020-07-14T02:25:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:27:06 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:27:06 prefetch.2.10.7: 'SRR11978232' is valid 2020-07-14T02:27:06 prefetch.2.10.7: 1) 'SRR11978232' was downloaded successfully 2020-07-14T02:27:06 prefetch.2.10.7: 'SRR11978232' has 0 unresolved dependencies Read 12589100 spots for SRR11978232/SRR11978232.sra Written 12589100 spots for SRR11978232/SRR11978232.sra 2020-07-14T02:28:02 prefetch.2.10.7: 1) Downloading 'SRR11978233'... 2020-07-14T02:28:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:29:25 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:29:25 prefetch.2.10.7: 'SRR11978233' is valid 2020-07-14T02:29:25 prefetch.2.10.7: 1) 'SRR11978233' was downloaded successfully 2020-07-14T02:29:25 prefetch.2.10.7: 'SRR11978233' has 0 unresolved dependencies Read 12458610 spots for SRR11978233/SRR11978233.sra Written 12458610 spots for SRR11978233/SRR11978233.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627610 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:11 49987964 reads; of these: 49987964 (100.00%) were unpaired; of these: 41447820 (82.92%) aligned 0 times 6490146 (12.98%) aligned exactly 1 time 2049998 (4.10%) aligned >1 times 17.08% overall alignment rate Time searching: 00:09:11 Overall time: 00:09:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2213134 / 8540144 = 0.2591 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 11:42:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 11:42:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:42:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:42:29: 1000000 INFO @ Tue, 14 Jul 2020 11:42:35: 2000000 INFO @ Tue, 14 Jul 2020 11:42:41: 3000000 INFO @ Tue, 14 Jul 2020 11:42:47: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 11:42:52: 5000000 INFO @ Tue, 14 Jul 2020 11:42:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 11:42:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:42:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:42:58: 6000000 INFO @ Tue, 14 Jul 2020 11:42:59: 1000000 INFO @ Tue, 14 Jul 2020 11:43:00: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:43:00: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:43:00: #1 total tags in treatment: 6327010 INFO @ Tue, 14 Jul 2020 11:43:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:43:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:43:00: #1 tags after filtering in treatment: 6327010 INFO @ Tue, 14 Jul 2020 11:43:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:43:00: #1 finished! INFO @ Tue, 14 Jul 2020 11:43:00: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:43:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:43:01: #2 number of paired peaks: 393 WARNING @ Tue, 14 Jul 2020 11:43:01: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 14 Jul 2020 11:43:01: start model_add_line... INFO @ Tue, 14 Jul 2020 11:43:01: start X-correlation... INFO @ Tue, 14 Jul 2020 11:43:01: end of X-cor INFO @ Tue, 14 Jul 2020 11:43:01: #2 finished! INFO @ Tue, 14 Jul 2020 11:43:01: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:43:01: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:43:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.05_model.r WARNING @ Tue, 14 Jul 2020 11:43:01: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:43:01: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:43:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:43:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:43:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:43:05: 2000000 INFO @ Tue, 14 Jul 2020 11:43:10: 3000000 INFO @ Tue, 14 Jul 2020 11:43:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:43:16: 4000000 INFO @ Tue, 14 Jul 2020 11:43:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:43:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:43:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.05_summits.bed INFO @ Tue, 14 Jul 2020 11:43:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1903 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 11:43:22: 5000000 INFO @ Tue, 14 Jul 2020 11:43:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 11:43:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:43:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:43:28: 6000000 INFO @ Tue, 14 Jul 2020 11:43:29: 1000000 INFO @ Tue, 14 Jul 2020 11:43:30: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:43:30: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:43:30: #1 total tags in treatment: 6327010 INFO @ Tue, 14 Jul 2020 11:43:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:43:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:43:30: #1 tags after filtering in treatment: 6327010 INFO @ Tue, 14 Jul 2020 11:43:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:43:30: #1 finished! INFO @ Tue, 14 Jul 2020 11:43:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:43:30: #2 number of paired peaks: 393 WARNING @ Tue, 14 Jul 2020 11:43:30: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 14 Jul 2020 11:43:30: start model_add_line... INFO @ Tue, 14 Jul 2020 11:43:30: start X-correlation... INFO @ Tue, 14 Jul 2020 11:43:30: end of X-cor INFO @ Tue, 14 Jul 2020 11:43:30: #2 finished! INFO @ Tue, 14 Jul 2020 11:43:30: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:43:30: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.10_model.r WARNING @ Tue, 14 Jul 2020 11:43:30: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:43:30: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:43:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:43:30: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:43:35: 2000000 INFO @ Tue, 14 Jul 2020 11:43:40: 3000000 INFO @ Tue, 14 Jul 2020 11:43:43: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:43:46: 4000000 INFO @ Tue, 14 Jul 2020 11:43:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:43:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:43:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.10_summits.bed INFO @ Tue, 14 Jul 2020 11:43:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (858 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:43:51: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:43:57: 6000000 INFO @ Tue, 14 Jul 2020 11:43:59: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:43:59: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:43:59: #1 total tags in treatment: 6327010 INFO @ Tue, 14 Jul 2020 11:43:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:43:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:43:59: #1 tags after filtering in treatment: 6327010 INFO @ Tue, 14 Jul 2020 11:43:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:43:59: #1 finished! INFO @ Tue, 14 Jul 2020 11:43:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:43:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:43:59: #2 number of paired peaks: 393 WARNING @ Tue, 14 Jul 2020 11:43:59: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 14 Jul 2020 11:43:59: start model_add_line... INFO @ Tue, 14 Jul 2020 11:44:00: start X-correlation... INFO @ Tue, 14 Jul 2020 11:44:00: end of X-cor INFO @ Tue, 14 Jul 2020 11:44:00: #2 finished! INFO @ Tue, 14 Jul 2020 11:44:00: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:44:00: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:44:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.20_model.r WARNING @ Tue, 14 Jul 2020 11:44:00: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:44:00: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:44:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:44:00: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:44:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:44:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:44:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:44:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:44:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521378/SRX8521378.20_summits.bed INFO @ Tue, 14 Jul 2020 11:44:19: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling